changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index f664710245ff265e184f922c642c0d3efc74a29a..bbdd2983490fc147ab64e1a26106922ba170d077 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -125,24 +125,24 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
                bool notgood = (b->core.flag & 0x0004) || (b2->core.flag & 0x0004);
 
                if (!notgood) {
-                 //swap if b is mate 2
-                 if (b->core.flag & 0x0080) {
-                   assert(b2->core.flag & 0x0040);
-                   bam1_t *tmp = b;
-                   b = b2; b2 = tmp;
-                 }
+                       //swap if b is mate 2
+                       if (b->core.flag & 0x0080) {
+                               assert(b2->core.flag & 0x0040);
+                               bam1_t *tmp = b;
+                               b = b2; b2 = tmp;
+                       }
 
-                 hit = wrapper.getNextHit();
-                 assert(hit != NULL);
+                       hit = wrapper.getNextHit();
+                       assert(hit != NULL);
 
-                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
-                 assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
+                       assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
+                       assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 
-                 convert(b, hit->getConPrb());
-                 convert(b2, hit->getConPrb());
+                       convert(b, hit->getConPrb());
+                       convert(b2, hit->getConPrb());
 
-                 b->core.mpos = b2->core.pos;
-                 b2->core.mpos = b->core.pos;
+                       b->core.mpos = b2->core.pos;
+                       b2->core.mpos = b->core.pos;
                }
 
                /*